Variational (VEM) analysis – To run a JDE-VEM analysis you need:
- paradigm csv file corresponding to your experimental design
- the preprocessed (spatially UNsmoothed) BOLD data associated with a single run [4D-Nifti file]
- the TR (in s) used at acquisition time
- a parcellation mask (if you normalize your data into MNI space, you can use the one provided with pyhrf)
If you want to use provided parcellation mask, check the path of the file by running:
and check for the
Then you can run:
$ pyhrf_jde_vem_analysis 2.5 stanford_willard_parcellation_3x3x3mm.nii.gz paradigm.csv bold_data_session1.nii
If you want to tune the parameters, check command line options (see commands). This is adviced to set the
dt parameter (the temporal resolution of the HRF) and the output folder.
check out the path of the files
$ pyhrf_jde_vem_analysis 2.4 subj0_parcellation.nii.gz paradigm_loc.csv subj0_bold_session0.nii.gz
replacing the files by their full path. This will create output files in the current folder. Check Visualization tools to check the outputs file.
- The multirun extension is currently under development and testing